#23580

Committed 25 Oct 2024 08:18PM CUT coverage: 21.187% (+0.3%) from 20.87%

Build # #23580

Build Type

Pull #10790

github

Committed by

web-flow

Commit Message

Merge ae058d107 into 5f5126a87

Pull Request Pull Request #10790: fix: issues in exporters and citations for PermaLink/non-DOI PIDs

Run Details

48 of 69 new or added lines in 7 files covered. (69.57%)

1410 existing lines in 14 files now uncovered.

18260 of 86183 relevant lines covered (21.19%)

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/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AbstractCreateDatasetCommand.java

package edu.harvard.iq.dataverse.engine.command.impl;

import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.dataset.DatasetType;
import edu.harvard.iq.dataverse.engine.command.CommandContext;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.pidproviders.PidProvider;
import static edu.harvard.iq.dataverse.util.StringUtil.isEmpty;
import java.io.IOException;
import java.util.Objects;
import java.util.logging.Logger;
import org.apache.solr.client.solrj.SolrServerException;

/**;
 * An abstract base class for commands that creates {@link Dataset}s.
 *
 * @author michael
 */
@RequiredPermissions(Permission.AddDataset)
public abstract class AbstractCreateDatasetCommand extends AbstractDatasetCommand<Dataset> {
    
    private static final Logger logger = Logger.getLogger(AbstractCreateDatasetCommand.class.getCanonicalName());
    
    final protected boolean harvested;
    final protected boolean validate;
    
    public AbstractCreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest) {
        this(theDataset, aRequest, false);
    }

    public AbstractCreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest, boolean isHarvested) {
        super(aRequest, theDataset);
        harvested=isHarvested;
        this.validate = true;
    }

    public AbstractCreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest, boolean isHarvested, boolean validate) {
        super(aRequest, theDataset);
        harvested=isHarvested;
        this.validate = validate;
    }
   
    protected void additionalParameterTests(CommandContext ctxt) throws CommandException {
        // base class - do nothing.
    }
    
    protected DatasetVersion getVersionToPersist( Dataset theDataset ) {
        return theDataset.getLatestVersion();
    }
    
    /**
     * Called after the dataset has been persisted, but before the persistence context
     * has been flushed. 
     * @param theDataset The em-managed dataset.
     * @param ctxt 
     * @throws edu.harvard.iq.dataverse.engine.command.exception.CommandException 
     */
    protected void postPersist( Dataset theDataset, CommandContext ctxt ) throws CommandException {
        // base class - default to nothing.
    }
    

    protected void postDBFlush( Dataset theDataset, CommandContext ctxt ) throws CommandException {
        // base class - default to nothing.
    }
    
    protected abstract void handlePid( Dataset theDataset, CommandContext ctxt ) throws CommandException ;
    
    @Override
    public Dataset execute(CommandContext ctxt) throws CommandException {
        
        additionalParameterTests(ctxt);
        
        Dataset theDataset = getDataset();
        PidProvider pidProvider = ctxt.dvObjects().getEffectivePidGenerator(theDataset);
        
        if ( isEmpty(theDataset.getIdentifier()) ) {
            pidProvider.generatePid(theDataset);
        }
        
        DatasetVersion dsv = getVersionToPersist(theDataset);
        // This re-uses the state setup logic of CreateDatasetVersionCommand, but
        // without persisting the new version, or altering its files. 
        new CreateDatasetVersionCommand(getRequest(), theDataset, dsv, validate).prepareDatasetAndVersion();
        
        if(!harvested) {
            checkSystemMetadataKeyIfNeeded(dsv, null);
        }

        registerExternalVocabValuesIfAny(ctxt, dsv);
        
        theDataset.setCreator((AuthenticatedUser) getRequest().getUser());
        
        theDataset.setCreateDate(getTimestamp());

        theDataset.setModificationTime(getTimestamp());
        for (DataFile dataFile: theDataset.getFiles() ){
            dataFile.setCreator((AuthenticatedUser) getRequest().getUser());
            dataFile.setCreateDate(theDataset.getCreateDate());
        }
        
        if (theDataset.getProtocol()==null) {
            theDataset.setProtocol(pidProvider.getProtocol());
        }
        if (theDataset.getAuthority()==null) {
            theDataset.setAuthority(pidProvider.getAuthority());
        }
        if (theDataset.getStorageIdentifier() == null) {
                String driverId = theDataset.getEffectiveStorageDriverId();
                theDataset.setStorageIdentifier(driverId  + DataAccess.SEPARATOR + theDataset.getAuthorityForFileStorage() + "/" + theDataset.getIdentifierForFileStorage());
        }
        if (theDataset.getIdentifier()==null) {
            pidProvider.generatePid(theDataset);
        }
        
        DatasetType defaultDatasetType = ctxt.datasetTypes().getByName(DatasetType.DEFAULT_DATASET_TYPE);
        DatasetType existingDatasetType = theDataset.getDatasetType();
        logger.fine("existing dataset type: " + existingDatasetType);
        if (existingDatasetType != null) {
            // A dataset type can be specified via API, for example.
            theDataset.setDatasetType(existingDatasetType);
        } else {
            theDataset.setDatasetType(defaultDatasetType);
        }
        
        // Attempt the registration if importing dataset through the API, or the app (but not harvest)
        handlePid(theDataset, ctxt);



        ctxt.em().persist(theDataset);
        
        postPersist(theDataset, ctxt);
        
        createDatasetUser(ctxt);
        
        theDataset = ctxt.em().merge(theDataset); // store last updates
        
        // DB updates - done.
        
        // Now we need the acutal dataset id, so we can start indexing.
        ctxt.em().flush();
        
        //Use for code that requires database ids
        postDBFlush(theDataset, ctxt);

        if (harvested) {
            try {
                ctxt.index().indexDataset(theDataset, true);
            } catch (SolrServerException | IOException solrEx) {
                logger.warning("Failed to index harvested dataset. " + solrEx.getMessage());
            }
        } else {
            // The asynchronous version does not throw any exceptions, 
            // logging them internally instead. 
            ctxt.index().asyncIndexDataset(theDataset, true);
        }
               
        return theDataset;
    }

    @Override
    public int hashCode() {
        return 97 + Objects.hashCode(getDataset());
    }

    @Override
    public boolean equals(Object obj) {
        if (obj == null) {
            return false;
        }
        if (!(obj instanceof AbstractCreateDatasetCommand)) {
            return false;
        }
        final AbstractCreateDatasetCommand other = (AbstractCreateDatasetCommand) obj;
        return Objects.equals(getDataset(), other.getDataset());
    }

    @Override
    public String toString() {
        return "[DatasetCreate dataset:" + getDataset().getId() + "]";
    }

}

1	package edu.harvard.iq.dataverse.engine.command.impl;
2
3	import edu.harvard.iq.dataverse.DataFile;
4	import edu.harvard.iq.dataverse.Dataset;
5	import edu.harvard.iq.dataverse.DatasetVersion;
6	import edu.harvard.iq.dataverse.authorization.Permission;
7	import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
8	import edu.harvard.iq.dataverse.dataaccess.DataAccess;
9	import edu.harvard.iq.dataverse.dataset.DatasetType;
10	import edu.harvard.iq.dataverse.engine.command.CommandContext;
11	import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
12	import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
13	import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
14	import edu.harvard.iq.dataverse.pidproviders.PidProvider;
15	import static edu.harvard.iq.dataverse.util.StringUtil.isEmpty;
16	import java.io.IOException;
17	import java.util.Objects;
18	import java.util.logging.Logger;
19	import org.apache.solr.client.solrj.SolrServerException;
20
21	/**;
22	* An abstract base class for commands that creates {@link Dataset}s.
23	*
24	* @author michael
25	*/
26	@RequiredPermissions(Permission.AddDataset)
27	public abstract class AbstractCreateDatasetCommand extends AbstractDatasetCommand<Dataset> {
28
UNCOV 29	private static final Logger logger = Logger.getLogger(AbstractCreateDatasetCommand.class.getCanonicalName());	×
30
31	final protected boolean harvested;
32	final protected boolean validate;
33
34	public AbstractCreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest) {
UNCOV 35	this(theDataset, aRequest, false);	×
UNCOV 36	}	×
37
38	public AbstractCreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest, boolean isHarvested) {
39	super(aRequest, theDataset);	×
40	harvested=isHarvested;	×
UNCOV 41	this.validate = true;	×
UNCOV 42	}	×
43
44	public AbstractCreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest, boolean isHarvested, boolean validate) {
45	super(aRequest, theDataset);	×
46	harvested=isHarvested;	×
UNCOV 47	this.validate = validate;	×
UNCOV 48	}	×
49
50	protected void additionalParameterTests(CommandContext ctxt) throws CommandException {
51	// base class - do nothing.
UNCOV 52	}	×
53
54	protected DatasetVersion getVersionToPersist( Dataset theDataset ) {
UNCOV 55	return theDataset.getLatestVersion();	×
56	}
57
58	/**
59	* Called after the dataset has been persisted, but before the persistence context
60	* has been flushed.
61	* @param theDataset The em-managed dataset.
62	* @param ctxt
63	* @throws edu.harvard.iq.dataverse.engine.command.exception.CommandException
64	*/
65	protected void postPersist( Dataset theDataset, CommandContext ctxt ) throws CommandException {
66	// base class - default to nothing.
UNCOV 67	}	×
68
69
70	protected void postDBFlush( Dataset theDataset, CommandContext ctxt ) throws CommandException {
71	// base class - default to nothing.
UNCOV 72	}	×
73
74	protected abstract void handlePid( Dataset theDataset, CommandContext ctxt ) throws CommandException ;
75
76	@Override
77	public Dataset execute(CommandContext ctxt) throws CommandException {
78
79	additionalParameterTests(ctxt);	×
80
UNCOV 81	Dataset theDataset = getDataset();	×
82	PidProvider pidProvider = ctxt.dvObjects().getEffectivePidGenerator(theDataset);	×
83
UNCOV 84	if ( isEmpty(theDataset.getIdentifier()) ) {	×
UNCOV 85	pidProvider.generatePid(theDataset);	×
86	}
87
UNCOV 88	DatasetVersion dsv = getVersionToPersist(theDataset);	×
89	// This re-uses the state setup logic of CreateDatasetVersionCommand, but
90	// without persisting the new version, or altering its files.
91	new CreateDatasetVersionCommand(getRequest(), theDataset, dsv, validate).prepareDatasetAndVersion();	×
92
UNCOV 93	if(!harvested) {	×
UNCOV 94	checkSystemMetadataKeyIfNeeded(dsv, null);	×
95	}
96
97	registerExternalVocabValuesIfAny(ctxt, dsv);	×
98
99	theDataset.setCreator((AuthenticatedUser) getRequest().getUser());	×
100
101	theDataset.setCreateDate(getTimestamp());	×
102
103	theDataset.setModificationTime(getTimestamp());	×
104	for (DataFile dataFile: theDataset.getFiles() ){	×
105	dataFile.setCreator((AuthenticatedUser) getRequest().getUser());	×
UNCOV 106	dataFile.setCreateDate(theDataset.getCreateDate());	×
107	}	×
108
UNCOV 109	if (theDataset.getProtocol()==null) {	×
110	theDataset.setProtocol(pidProvider.getProtocol());	×
111	}
UNCOV 112	if (theDataset.getAuthority()==null) {	×
113	theDataset.setAuthority(pidProvider.getAuthority());	×
114	}
115	if (theDataset.getStorageIdentifier() == null) {	×
UNCOV 116	String driverId = theDataset.getEffectiveStorageDriverId();	×
117	theDataset.setStorageIdentifier(driverId + DataAccess.SEPARATOR + theDataset.getAuthorityForFileStorage() + "/" + theDataset.getIdentifierForFileStorage());	×
118	}
UNCOV 119	if (theDataset.getIdentifier()==null) {	×
UNCOV 120	pidProvider.generatePid(theDataset);	×
121	}
122
123	DatasetType defaultDatasetType = ctxt.datasetTypes().getByName(DatasetType.DEFAULT_DATASET_TYPE);	×
124	DatasetType existingDatasetType = theDataset.getDatasetType();	×
UNCOV 125	logger.fine("existing dataset type: " + existingDatasetType);	×
126	if (existingDatasetType != null) {	×
127	// A dataset type can be specified via API, for example.
128	theDataset.setDatasetType(existingDatasetType);	×
129	} else {
UNCOV 130	theDataset.setDatasetType(defaultDatasetType);	×
131	}
132
133	// Attempt the registration if importing dataset through the API, or the app (but not harvest)
UNCOV 134	handlePid(theDataset, ctxt);	×
135
136
137
138	ctxt.em().persist(theDataset);	×
139
140	postPersist(theDataset, ctxt);	×
141
142	createDatasetUser(ctxt);	×
143
UNCOV 144	theDataset = ctxt.em().merge(theDataset); // store last updates	×
145
146	// DB updates - done.
147
148	// Now we need the acutal dataset id, so we can start indexing.
UNCOV 149	ctxt.em().flush();	×
150
151	//Use for code that requires database ids
152	postDBFlush(theDataset, ctxt);	×
153
154	if (harvested) {	×
155	try {
UNCOV 156	ctxt.index().indexDataset(theDataset, true);	×
UNCOV 157	} catch (SolrServerException \| IOException solrEx) {	×
UNCOV 158	logger.warning("Failed to index harvested dataset. " + solrEx.getMessage());	×
159	}	×
160	} else {
161	// The asynchronous version does not throw any exceptions,
162	// logging them internally instead.
UNCOV 163	ctxt.index().asyncIndexDataset(theDataset, true);	×
164	}
165
UNCOV 166	return theDataset;	×
167	}
168
169	@Override
170	public int hashCode() {
171	return 97 + Objects.hashCode(getDataset());	×
172	}
173
174	@Override
175	public boolean equals(Object obj) {
176	if (obj == null) {	×
UNCOV 177	return false;	×
178	}
UNCOV 179	if (!(obj instanceof AbstractCreateDatasetCommand)) {	×
UNCOV 180	return false;	×
181	}
UNCOV 182	final AbstractCreateDatasetCommand other = (AbstractCreateDatasetCommand) obj;	×
UNCOV 183	return Objects.equals(getDataset(), other.getDataset());	×
184	}
185
186	@Override
187	public String toString() {
UNCOV 188	return "[DatasetCreate dataset:" + getDataset().getId() + "]";	×
189	}
190
191	}

IQSS / dataverse / #23580

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